IMP Reference Guide
2.20.2
The Integrative Modeling Platform
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Score the improper dihedral based on a UnaryFunction,. More...
#include <IMP/atom/ImproperSingletonScore.h>
Score the improper dihedral based on a UnaryFunction,.
This scores the improper dihedral using information stored in its Dihedral decorator. The score is based on the difference between the stored ideal improper angle and the actual angle and scaled by the stiffness. That is stiffness * (improper_angle-ideal_value). The difference is in radians between -pi and +pi; it is the shortest distance from one angle to the other.
Just as for regular dihedral angles, the improper angle is defined as the angle between the plane in which the first three atoms lie and the plane in which the last three atoms lie.
Definition at line 35 of file ImproperSingletonScore.h.
Public Member Functions | |
ImproperSingletonScore (UnaryFunction *f) | |
Use f to penalize deviations in angle. More... | |
virtual ModelObjectsTemp | do_get_inputs (Model *m, const ParticleIndexes &pis) const override |
Overload this method to specify the inputs. More... | |
double | evaluate_if_good_indexes (Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const override |
virtual double | evaluate_index (Model *m, ParticleIndex p, DerivativeAccumulator *da) const override |
Compute the score and the derivative if needed. More... | |
double | evaluate_indexes (Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const overridefinal |
Compute the score and the derivative if needed over a set. More... | |
double | evaluate_indexes_delta (Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const overridefinal |
Compute the change in score and the derivative if needed over a set. More... | |
double | evaluate_indexes_scores (Model *m, const ParticleIndexes &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const overridefinal |
Compute the score and the derivative if needed over a set. More... | |
virtual std::string | get_type_name () const override |
virtual ::IMP::VersionInfo | get_version_info () const override |
Get information about the module and version of the object. More... | |
Public Member Functions inherited from IMP::SingletonScore | |
SingletonScore (std::string name="SingletonScore %1%") | |
Restraints | create_current_decomposition (Model *m, ParticleIndex vt) const |
virtual double | evaluate_if_good_index (Model *m, ParticleIndex vt, DerivativeAccumulator *da, double max) const |
Compute the score and the derivative if needed, only if "good". More... | |
Public Member Functions inherited from IMP::ParticleInputs | |
ModelObjectsTemp | get_inputs (Model *m, const ParticleIndexes &pis) const |
Get the ModelObjects read when the given list of particles is used. More... | |
Public Member Functions inherited from IMP::Object | |
virtual void | clear_caches () |
CheckLevel | get_check_level () const |
LogLevel | get_log_level () const |
void | set_check_level (CheckLevel l) |
void | set_log_level (LogLevel l) |
Set the logging level used in this object. More... | |
void | set_was_used (bool tf) const |
void | show (std::ostream &out=std::cout) const |
const std::string & | get_name () const |
void | set_name (std::string name) |
Additional Inherited Members | |
Public Types inherited from IMP::SingletonScore | |
typedef Particle * | Argument |
typedef ParticleIndex | IndexArgument |
typedef SingletonModifier | Modifier |
typedef Particle * | PassArgument |
typedef ParticleIndex | PassIndexArgument |
Protected Member Functions inherited from IMP::SingletonScore | |
virtual Restraints | do_create_current_decomposition (Model *m, ParticleIndex vt) const |
Override this to return your own decomposition. More... | |
Protected Member Functions inherited from IMP::Object | |
Object (std::string name) | |
Construct an object with the given name. More... | |
virtual void | do_destroy () |
IMP::atom::ImproperSingletonScore::ImproperSingletonScore | ( | UnaryFunction * | f | ) |
Use f to penalize deviations in angle.
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overridevirtual |
Overload this method to specify the inputs.
Implements IMP::ParticleInputs.
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overridevirtual |
Compute the score and the derivative if needed over a set, only if "good". This functions similarly to evaluate_indexes(), but may terminate the computation early if the total score is higher than max.
Reimplemented from IMP::SingletonScore.
Definition at line 45 of file ImproperSingletonScore.h.
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overridevirtual |
Compute the score and the derivative if needed.
m | the model of vt |
vt | the index in m of an object of type Particle |
da | a DerivativeAccumulator that weights computed derivatives. If nullptr, derivatives will not be computed. |
Implements IMP::SingletonScore.
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finaloverridevirtual |
Compute the score and the derivative if needed over a set.
m | the model of o |
o | objects of type Particle, specified by index |
da | a derivative accumulator that weights computed derivatives. If nullptr, derivatives will not be computed. |
lower_bound | index of first item in o to evaluate |
upper_bound | index one past last item in o to evaluate |
Reimplemented from IMP::SingletonScore.
Definition at line 45 of file ImproperSingletonScore.h.
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finaloverridevirtual |
Compute the change in score and the derivative if needed over a set.
The score for each o[indexes[x]] is updated in score[indexes[x]] and the total difference between the old and new score values (over the set) is returned.
Reimplemented from IMP::SingletonScore.
Definition at line 45 of file ImproperSingletonScore.h.
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finaloverridevirtual |
Compute the score and the derivative if needed over a set.
Like regular evaluate_indexes(), but the score for each o[x] is also returned as score[x].
Reimplemented from IMP::SingletonScore.
Definition at line 45 of file ImproperSingletonScore.h.
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overridevirtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 46 of file ImproperSingletonScore.h.